Actually, the Iron Patriot armor is a completely different armor from the War Machine we saw in Iron Man 2.
According to the prequel comic, sometime after Iron Man 2, Tony got the Hammer War Machine back from Rhodey and took off all the the Hammer additions and got his Mark II back.
He surprised Rhodey with a new War Machine armor.

When the Mandarin attacks started, the government got AIM to do a software upgrade and the red, white, and blue paint job for it.